Genome-wide essential gene identification in Streptococcus sanguinis

A clear perception of gene essentiality in bacterial pathogens is pivotal for identifying drug targets to combat emergence of new pathogens and antibiotic-resistant bacteria, for synthetic biology, and for understanding the origins of life. We have constructed a comprehensive set of deletion mutants and systematically identified a clearly defined set of essential genes for Streptococcus sanguinis. Our results were confirmed by growing S. sanguinis in minimal medium and by double-knockout of paralogous or isozyme genes. Careful examination revealed that these essential genes were associated with only three basic categories of biological functions: maintenance of the cell envelope, energy production, and processing of genetic information. Our finding was subsequently validated in two other pathogenic streptococcal species, Streptococcus pneumoniae and Streptococcus mutans and in two other gram-positive pathogens, Bacillus subtilis and Staphylococcus aureus. Our analysis has thus led to a simplified model that permits reliable prediction of gene essentiality

Network Compression as a Quality Measure for Protein Interaction Networks

With the advent of large-scale protein interaction studies, there is much debate about data quality. Can different noise levels in the measurements be assessed by analyzing network structure? Because proteomic regulation is inherently co-operative, modular and redundant, it is inherently compressible when represented as a network. Here we propose that network compression can be used to compare false positive and false negative noise levels in protein interaction networks. We validate this hypothesis by first confirming the detrimental effect of false positives and false negatives. Second, we show that gold standard networks are more compressible. Third, we show that compressibility correlates with co-expression, co-localization, and shared function. Fourth, we also observe correlation with better protein tagging methods, physiological expression in contrast to over-expression of tagged proteins, and smart pooling approaches for yeast two-hybrid screens. Overall, this new measure is a proxy for both sensitivity and specificity and gives complementary information to standard measures such as average degree and clustering coefficients

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein

Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In Gram-negative bacteria, ∼30–60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships

Tight Time-Space Lower Bounds for Finding Multiple Collision Pairs and Their Applications

We consider a collision search problem (CSP), where given a parameter $C$, the goal is to find $C$ collision pairs in a random function $f:[N] \rightarrow [N]$ (where $[N] = \{0,1,\ldots,N-1\})$ using $S$ bits of memory. Algorithms for CSP have numerous cryptanalytic applications such as space-efficient attacks on double and triple encryption. The best known algorithm for CSP is parallel collision search (PCS) published by van Oorschot and Wiener, which achieves the time-space tradeoff $T^2 \cdot S = \tilde{O}(C^2 \cdot N)$ for $S = \tilde{O}(C)$. In this paper, we prove that any algorithm for CSP satisfies $T^2 \cdot S = \tilde{\Omega}(C^2 \cdot N)$ for $S = \tilde{O}(C)$, hence the best known time-space tradeoff is optimal (up to poly-logarithmic factors in $N$). On the other hand, we give strong evidence that proving similar unconditional time-space tradeoff lower bounds on CSP applications (such as breaking double and triple encryption) may be very difficult, and would imply a breakthrough in complexity theory. Hence, we propose a new restricted model of computation and prove that under this model, the best known time-space tradeoff attack on double encryption is optimal

Prevalence of physical activity through the practice of sports among adolescents from Portuguese speaking countries

This study evaluated the prevalence of physical activity through the practice of sports in adolescents from schools in two Brazilian cities and a Portuguese school, and its association with independent variables, such as gender and age. A cross-sectional study was conducted of schoolchildren from two cities in Brazil and one in Portugal. The total study sample was 3694 subjects (1622 males and 1872 females). Physical activity levels were assessed using Baecke's questionnaire. Body weight was measured on electronic scales and stature was measured with a portable wooden stadiometer. Numerical variables were expressed as mean, categorical variables were expressed as percentages and the chi-square test analyzed associations. The prevalence of no sport was high (39.7%), being higher in the Portuguese school than in the Brazilian schools (p < 0.001). Irrespective of being an adolescent in a Brazilian or Portuguese school, boys showed higher engagement in sports practice than girls (p < 0.001). In both, differences were identified between adolescents aged 13 to 15 (P = 0.001) and 16 to 17 (P = 0.001). The prevalence of physical inactivity among schoolchildren from two cities in Brazil and a school in Portugal was high, with the girls practicing less sport than the boys and with this imbalance likely to be higher in adolescents